StemBase

Stem Cell Network

Microarray Course, Unit 6

June 2007

Sections

• Introduction to StemBase

• Using StemBase

• Introduction to Biomarker server

• Using the Biomarker server

Introduction to StemBase

http://www.stembase.ca

The Stem Cell Genomics Project

• Objective: acquire a complete understanding of the genetic factors that:– specify stem cell identity and function; and– regulate commitment and differentiation

• Rationale:– Stem cells play an essential role in the human body as

they provide the starting material for every organ and tissue

– Knowledge of regulatory genes acting in and on stem cells is necessary to exploit their full therapeutic potential

STEM CELL NETWORK+20 GROUPS

OHRI – GENOMICS PLATFORMDNA microarray / SAGE / Proteomics

Bioinformatics Group

StemBase

samples

data

data

PUBLIC

SCN Sample Contributors• Jane Aubin• Mick Bhatia• John Dick• Connie Eaves• Jacques Galipeau• Alain Garnier• Marina Gertsentein• John Hassell• Keith Humphries• Norman Iscove• Michael McBurney

• Lynn Megeney• James Piret• Derrick Rancourt• Janet Rossant• Michael Rudnicki• Luc Sabourin• JP Tremblay• T. Michael Underhill• Valerie Wallace• Peter Zandstra

StemBaseDatabase of gene expression data in mouse and human stem cells

Affymetrix DNA microarray data (225 samples) and SAGE (6 samples)

Study genes important for stem cell function

Perez-Iratxeta, C., G. Palidwor, C.J. Porter, N.A. Sanche, M.R. Huska, B.P. Suomela, E.M. Muro, P. Krzyzanowski, E. Hughes, P.A. Campbell, M.A. Rudnicki and M.A. Andrade (2005) Study of stem cell function using microarray experiments. FEBS Letters. 579, 1795-1801.

Species

Tissue Types

184

44

3

Mouse

Human

Rat

Blastocyst, 20

Blood, 5

Bone marrow, 31

Brain, 7

Calvaria, 3

Cervical epith., 3Ciliary margin eye, 4

Cordblood, 11

Dermis, 1

Embryonic, 42

Fetal cells, 38

Fibroblast, 4Kidney, 1

Mammary, 14

Muscle, 42

Retina, 3Adipose tissue, 1

Genes expressed in:

80%-100%of all samples

0%-20%of all

samples mitotic chromosome condensation0.0348GO:0007076

dendrite morphogenesis 0.0204GO:0016358

synaptogenesis0.0134GO:0007416

calcium channel regulator activity0.00362GO:0005246

G-protein coupled receptor activity, unknown ligand 3.40E-11GO:0016526

establishment of protein localization3.50E-22GO:0045184

RNA splicing1.79E-22GO:0008380

cellular metabolism4.31E-27GO:0044237

protein biosynthesis3.03E-28GO:0006412

mitochondrion9.43E-31GO:0005739

RNA binding1.40E-42GO:0003723

ribonucleoprotein complex1.83E-66GO:0030529

GO as namePvalueGO

Dermis

AdiposeNeural

Myoblasts

Bone marrow

Bone marrowMuscle

Myospheres

Bone marrow

Osteoblasts

Retinal primary

Retinal first passageMammospheres

Mammospheres undifferenciated

Neurospheres

Bone marrow

CancerR1 serum64

Cancer

Cancer Embyoid bodies

R1 serum6999 D4D

D4EEmbyoid bodiesJ1C2E

D4AR1V6.5

C2D Embyoid bodiesC2A

Dim1

Dim2

Mouse / MOE430

Dim1

Dim2

Cord blood

Bone marrow

Cord blood

Bone marrowCord blood

Peripheral

PeripheralFetal

Myoblasts

I6

Retinal first passage

Myoblasts differentiated

Retinal primary

HelaHela

M-O7eM-O7e

M-O7e Smad7

Kidney

I6

Human / HGU133

Public web serverhttp://www.scgp.ca:8080/StemBase/

Marker detection

Use microarray data to identify probe sets that can act as markers.

What and how they mark is a separate issue.

Krzyzanowski and Andrade (2007) Identification of novel stem cell markers using gap analysis of gene expression data. Submitted.

Method Overview

• Identification– Find probe sets which appear to divide samples

into two groups binary classifications

Method Overview

• Identification– Find probe sets which appear to divide samples

into two groups binary classifications

• Cluster expansion– Identify clusters of probe sets which support binary

classifications

• Receiver Operator Characteristic (ROC) curves are used to generate clusters of probe sets with expression patterns which can reproduce each binary classification.

1402235_at

“Pattern X”1101100101101110

Proposed markers for “Pattern X”

Probe set Score

1402235_at 1.00000

1409748_at 1.00000

1430293_x_at 0.99302

…

1427392_a_at 0.90021

embryonic hematopoieticP19 spheresfibroblastosteoblast

Five fold enrichment on 71 stem cell markers. From 71 in about 30,000 genes to 49 in 4,449 genes

http://www.ogic.ca/projects/markerserver/enter.php

Pointers

• StemBase. http://www.stembase.ca

• Biomarker server. http://www.ogic.ca/projects/markerserver

• Thanks for your attention!